View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Research Online University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2012 Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target Andrew Robinson University of Wollongong, [email protected] Rebecca J. Causer University of Wollongong, [email protected] Nicholas E. Dixon University of Wollongong, [email protected] Follow this and additional works at: https://ro.uow.edu.au/scipapers Part of the Life Sciences Commons, Physical Sciences and Mathematics Commons, and the Social and Behavioral Sciences Commons Recommended Citation Robinson, Andrew; Causer, Rebecca J.; and Dixon, Nicholas E.: Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target 2012, 352-372. https://ro.uow.edu.au/scipapers/2996 Research Online is the open access institutional repository for the University of Wollongong. For further information contact the UOW Library: [email protected] Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target Abstract "New antibiotics with novel modes of action are required to combat the growing threat posed by multi- drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad- spectrum antibacterials. DNA replication is a conserved and essential process, and the large number of proteins that interact to replicate DNA in bacteria are distinct from those in eukaryotes and archaea; yet none of the antibiotics in current clinical use acts directly on the replication machinery. Bacterial DNA synthesis thus appears to be an underexploited drug target. However, before this system can be targeted for drug design, it is important to understand which parts are conserved and which are not, as this will have implications for the spectrum of activity of any new inhibitors against bacterial species, as well as the potential for development of drug resistance. In this review we assess similarities and differences in replication components and mechanisms across the bacteria, highlight current progress towards the discovery of novel replication inhibitors, and suggest those aspects of the replication machinery that have the greatest potential as drug targets." Keywords architecture, drug, underexploited, machinery, replication, dna, bacterial, conservation, target, CMMB Disciplines Life Sciences | Physical Sciences and Mathematics | Social and Behavioral Sciences Publication Details Robinson, A., Causer, R. J. & Dixon, N. E. (2012). Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target. Current Drug Targets, 13 (3), 352-372. This journal article is available at Research Online: https://ro.uow.edu.au/scipapers/2996 352 Current Drug Targets, 2012, 13, 352-372 Architecture and Conservation of the Bacterial DNA Replication Machinery, an Underexploited Drug Target Andrew Robinson, Rebecca J. Causer and Nicholas E. Dixon* School of Chemistry, University of Wollongong, Australia Abstract: New antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad-spectrum antibacterials. DNA replication is a conserved and essential process, and the large number of proteins that interact to replicate DNA in bacteria are distinct from those in eukaryotes and archaea; yet none of the antibiotics in current clinical use acts directly on the replication machinery. Bacterial DNA synthesis thus appears to be an underexploited drug target. However, before this system can be targeted for drug design, it is important to understand which parts are conserved and which are not, as this will have implications for the spectrum of activity of any new inhibitors against bacterial species, as well as the potential for development of drug resistance. In this review we assess similarities and differences in replication components and mechanisms across the bacteria, highlight current progress towards the discovery of novel replication inhibitors, and suggest those aspects of the replication machinery that have the greatest potential as drug targets. Keywords: DnaB, DnaC, DnaE, DNA polymerase IIIC, DnaG primase, helicase. INTRODUCTION 17]. High-throughput genome sequencing initiatives have generated more than 1000 complete bacterial genomes [18]. The overuse of antibiotics during the past 60 years has Many hundreds more are near completion. High-throughput exerted strong selective pressure on pathogenic bacteria, dri- gene knockout studies have been used to determine the ving many to develop effective mechanisms of drug resist- essentiality of each individual gene in 14 different bacterial ance [1]. Among the most notorious examples are methici- species [14]. For well-studied model organisms, such as llin-resistant strains of Staphylococcus aureus (MRSA) and Escherichia coli, large-scale attempts are being made to map vancomycin-resistant Enterococcus spp. (VRE), both Gram- the entire cellular protein-protein interaction network [19]. positives. An equal or perhaps greater threat, however, Structural genomics initiatives have now determined three- comes from Gram-negative bacteria like Acinetobacter and dimensional structures for many hundreds of bacterial Pseudomonas spp., some strains of which are multi- or even proteins [15]. In addition to these high-throughput studies, pan-drug resistant [2-4]. Resistant bacteria have developed researchers using more traditional approaches have made diverse strategies to evade antibiotic therapy and most many exciting discoveries in recent years. A highlight is the worryingly, appear to be developing resistance against an use of fluorescence microscopy to study the actions of ever-widening spectrum of antibiotic compounds [5]. There individual proteins inside living bacterial cells, which has is thus an urgent need for the development of new antibiotics added clarity to support decades of in vitro studies [20]. with entirely new modes of action to treat infections caused Crucially, the data derived from genome sequencing and by these highly resistant bacteria [1, 2, 6-8]. Unfortunately, other high-throughput studies now allow us to extrapolate the development of novel antimicrobial compounds has all much of the information derived from traditional work with but ceased in recent years, in part because existing antibio- model organisms to other bacteria, including species that act tics were so effective prior to the widespread dissemination as human pathogens [21]. of drug resistant strains [2, 9]. Efforts to develop entirely novel antibiotics have been hampered by the inherent diffi- Are there new opportunities for the discovery of novel culty of discovering appropriate cellular targets and func- antibiotic compounds buried within all these new data? Now tional lead compounds. Most antibiotics developed in recent is an ideal time to collate this information and use it to assess years have been simple modifications of older compounds, which among cellular processes might serve as useful targets aimed primarily at circumventing problems with resistance for drug discovery studies. In general, the biological targets [10]. of antibiotics are: (i) essential for growth and propagation of bacterial cells, (ii) conserved across a wide range of human The past decade has seen an explosion of data that pathogens, and (iii) not present, or distinct from correspond- greatly enhance our knowledge of bacterial physiology [11- ing processes, in humans. Promisingly, there remain some cellular systems in bacteria that satisfy these criteria, yet are *Address correspondence to this author at the School of Chemistry, not the targets of any current antibiotics. These systems University of Wollongong, NSW 2522, Australia; Tel: (61)-2-42214346; might therefore include new targets for the rational design or Fax: (61)-2-42214287; E-mail: [email protected] discovery of novel antibiotic compounds. 1389-4501/12 $58.00+.00 © 2012 Bentham Science Publishers Bacterial DNA Replication as a Drug Target Current Drug Targets, 2012, Vol. 13, No. 3 353 The replication of chromosomal DNA is one such pro- contain tightly bound ATP or ADP. The origin contains a cess. It is one of the most fundamental processes carried out series of five 9-bp sequence repeats known as DnaA (or R) by bacteria, yet currently only one functional class of anti- boxes, to which DnaA-ATP and DnaA-ADP bind, as well as biotics (the DNA gyrase inhibitors) targets DNA replication, three additional sites (I boxes) that are specific for the ATP- and even then the mode of action is indirect [22]. The bound form [34, 35]. DnaA appears to remain associated mechanisms underlying bacterial